GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Azorhizobium caulinodans ORS 571

Align Imidazole glycerol phosphate synthase subunit HisH 1; EC 4.3.2.10; IGP synthase glutaminase subunit 1; EC 3.5.1.2; IGP synthase subunit HisH 1; ImGP synthase subunit HisH 1; IGPS subunit HisH 1 (uncharacterized)
to candidate WP_012172228.1 AZC_RS19080 glutamine-hydrolyzing GMP synthase

Query= curated2:Q7MLS3
         (204 letters)



>NCBI__GCF_000010525.1:WP_012172228.1
          Length = 515

 Score = 41.2 bits (95), Expect = 3e-08
 Identities = 35/114 (30%), Positives = 53/114 (46%), Gaps = 12/114 (10%)

Query: 101 VECLGLCDGEVKLLQT--GDLPLPH---MGWNTVSAKAGNPLFKGI-EEGEYFYFVHSFA 154
           +  LG+C GE  +     G +   H    G   V       LF+G+ +EG+ +    S  
Sbjct: 75  IPVLGICYGEQAMADQLGGKVEAGHHREFGRAEVEVVKPAALFEGVWQEGQRYLVWMSHG 134

Query: 155 -----MPVGDYTIAECEYGNSFTAAVQSGNYYGVQFHPE-RSSKAGAKLIQNFL 202
                +P G   IA+ E       A +S  +YGVQFHPE   +  GA+L++NF+
Sbjct: 135 DRVTQLPAGFEVIAQSENAPFAAIADESRKFYGVQFHPEVVHTPQGAQLLRNFV 188


Lambda     K      H
   0.317    0.136    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 217
Number of extensions: 15
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 204
Length of database: 515
Length adjustment: 28
Effective length of query: 176
Effective length of database: 487
Effective search space:    85712
Effective search space used:    85712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory